Lost Years
by Kodiak Sage
Summary: What if Commander Shepard and Kaidan had had more time to talk and meet privately on Horizon and through the rest of ME2? Can anything make up for those two lost years between them? Starts out reworking the Horizon cut scene, then continues throughout the ME2 storyline. Shepard(F)/Kaidan


**Lost Years**

What if Commander Shepard and Kaidan had had more time to talk and meet privately on Horizon and through the rest of ME2? Can anything make up for those two lost years between them? Starts out reworking the Horizon cut scene, then continues throughout the ME2 storyline. Shepard(F)/Kaidan

Warning: Some Sexual Content

* * *

"Shepard…I know that name." The cowardly tech gritted his teeth and stared extra hard at me through his watery little eyes.

A deep, serious voice cut into the conversation out of nowhere. "That's Commander Shepard of the Normandy. You're talking to a legend."

"Kaidan." My heart seemed to pause for a second while I looked him over. He looked just like he did when I had seen him last—dark, serious eyes, military cropped hair, even if his armor was newer and better. The two years seemed to have just slipped past him, leaving him the same Kaidan who as in the picture on my desk on the Normandy, the same Kaidan as I had in my cabin the night before Ilium, the same Kaidan I had ached to see ever since my eyes opened in that hellish Cerberus lab.

He stepped forward and put his arms around me before I could think of anything to say. I was still reeling from the surprise of finding him here. All I could do was breathe in the scent of his sweat and shampoo and armor, and then we were at arm's length again and he was telling me how hard the last two years had been for him, as if it was my fault.

"Excuse me," I addressed Garrus and Miranda, who were standing behind me, "I need a word alone with Lieutenant Alenko."

"It's Commander now," Kaidan corrected.

"Right."

Garrus gave me a significant look and walked away to examine his gun. Miranda raised a haughty eyebrow and traipsed in the other direction.

"So if you're not dead, then where have you been for the last two years? Why didn't you contact me?"

"I spent the last two years in a coma in a Cerberus lab. I've only been up and kicking for about a month now."

"Cerberus." Kaidan's voice was venom. He looked me up and down, as if expecting me to suddenly attack him. "I can't believe it. You—and Garrus—how could you?"

"I have to do what I have to do. They brought me back, gave me a ship and a crew—they want to help the colonies just like you do."

"So you're their lapdog now?" Kaidan asked, disgust apparent on his handsome features.

"Who are you talking to? When have I ever just done what I was told? I don't trust these Cerberus bastards any more than you do Kaidan, but I'm not going to just turn down resources that can help me do my job." My temper was flaring, and this was going wrong—all wrong. I didn't want to fight with Kaidan, I wanted to make up with him—I wanted him to be glad to see me, to jump in and join my cause. I wanted him on my side again.

"And what about us?" I asked. My voice dropped to a near whisper. "Don't you care about that at all? Do you really think I could change so much?"

"Change, Shepard? It's been two years. A hell of a lot can change about a person in two years."

"I wasn't even awake for those two years! As far as I'm concerned, that night on Ilium…that was months ago, not years ago."

Kaidan's face was hard and cold. He was looking at me like I was a distasteful statue. I stepped in closer, right into his personal space. Our armor clinked and I reached a hand up to touch his face. He flinched away from it, but his eyes were downcast, guilty.

"I don't know that you're the same Shepard I knew. I've moved on, more or less."

"Look me in the eyes and tell me that what we had doesn't mean anything." My voice was quiet, but commanding. I wasn't going to let him go so easily.

He looked up and met my gaze, but I knew what he was going to say before he even opened his mouth.

"I'm sorry Shepard."

I leaned in and kissed him, one last desperate attempt to convince him of how serious I was. I expected him to flinch away like he had from my touch, or to be an unmoving nonparticipant, but to my surprise his lips were warm and open and inviting. I felt his hand move to my waist, and he tilted his head to kiss me back. I could feel his passion and hopefulness in those actions, even if his words had rejected me.

Garrus cleared his throat from behind us. "The Kodiak is ready to pick us up Commander."

Kaidan pulled away from me abruptly. He looked troubled by his own reaction. "I have to think about this Shepard. Maybe…we can meet up on the citadel when we get a chance and talk again."

I was only off balance for a moment, and then I was back on Horizon, a colony emptied by the Collectors, leading my squad of commandos to find out what had happened. I suddenly felt rushed, adrenaline pumping through my veins, my cheeks flushing. I wanted to get back to the Normandy and process everything that had happened.

"I'll contact you." I said quickly, before turning and following Garrus to the shuttle pick-up.

Once we were on board, Miranda and Garrus both respected my space and my silence.

I didn't cry until I made it up to my cabin.

#

After a few days, thinking about Kaidan made me so angry that I couldn't decide if I wanted to beat his ass or fuck his brains out. How could he doubt me? I'd pulled his ass out of the fire, I'd been there for some of the best and worst moments of both of our lives, and…that night before Ilium, I thought that we had established some kind of connection beyond Commander and Lieutenant, regulations be damned.

His apology letter didn't help much, though it softened me some. I did my best to put him out of my mind completely until I had another reason to go to the citadel. Maybe we could work things out in person now that things were more out in the open.

The Normandy was docked at the Citadel and the crew was released for 24 hour shore leave. I had just finished up some business with Thane and planned to spend the rest of the break in my cabin, sleeping and exercising and avoiding everyone I could, but something stopped me from shutting down my terminal right away. For some reason I just couldn't let go of that small hope I had that I could still fix things with Kaidan. I entered a search to see if Kaidan's ship was docked on the citadel. It was.

"EDI, get the coordinates of Commander Alenko on the Citadel and forward them to my omni tool."

"Right away Commander."

I wore plain black ship-fatigues of Cerberus issue but without any damning Cerberus insignia or logos. I wished more than anything that I could wear my N7 armor and pack all my guns as if this were any other mission. Who said that attacks on the heart were any less dangerous than an armor-piercing round to the head? At least with my Spectre status reinstated I wouldn't have to forgo my pistol tucked under my shirt, but full armor would have been best.

According to the coordinates, Kaidan was just outside the C-sec offices on the Zakara ward. It was amazing that I hadn't run into him when I was out with Thane only a few hours ago.

I spotted him before he spotted me. He must have been on business because he was in his flashiest Alliance uniform, the kind with the gold trim and the big buttons. His rank winked from his collar impressively, and caught the eyes of many a passerby. I sidled up, incognito in my blacks.

"Commander Alenko." I said quietly.

"Shepard!" He was surprised, but he didn't immediately turn away in disgust, which was a good sign.

"What are you doing here?" I asked. My eyes flicked up and down his well-built form.

"Business. I'm trying to convince C-sec to give the Alliance access to their criminal database so we can track people who have been using the colonies disappearances to launder money, but so far I've only met dead ends."

"I might be able to help. I know Captain Bailey here, he might be able to get you access."

Without waiting for a response, I sauntered over to Captain Bailey's office and explained the situation.

His gruff voice indicated assent. "Of course Shepard. You being a Spectre, requisitions such as this are totally legal. Who you hand these files over to is your business." He downloaded the information onto a datapad and handed it over. I turned to Kaidan and passed it to him.

"I forgot how everyone around you just molds to your will Shepard," he said with a little bit of envy.

"Captain Bailey, do you mind if we use your private office back there for a few minutes? Commander Alenko and I need to discuss something."

"It's all yours Commander," Bailey said.

Kaidan followed me into the office without protest. He knew as well as I that this conversation couldn't wait.

The office was dimly lit, and I left it that way. I sat back against the desk and crossed my arms over my chest. Kaidan stood across from me, likewise situated. I had 18 hours before I had to be back aboard the Normandy, and I was going to hash this out with Kaidan even if it took every minute of those 18 hours.

"Well Shepard, I've heard a little bit about some of your missions. I still think that working with Cerberus is a bad idea, but I have to admit that you seem to be making progress towards finding the collectors. Getting ahold of that Reaper IFF couldn't have been easy."

"It wasn't." I said, arching an eyebrow at him. Said IFF was currently being installed in the Normandy, and I was a little bit dismayed that Kaidan and the Alliance knew about the top-secret tech at all.

"So you're really going to do it? You're going through the Omega 4 relay?"

"Of course." I said.

Kaidan dropped his arms to his side and started pacing, short sharp steps across the office. His jaw was jutting and his broody brows were furrowed. "Shepard, that's…that's a suicide mission!"

"I know that there's a chance we might not make it back," I admitted. When he paced closest to me, I grabbed his forearm, stopping him in his tracks. "But dammit Kaidan, if there is a way to get back, I will. I haven't spent all this time traipsing about the galaxy for shits and giggles. I'm assembling a team who will be able to take out the collectors and get us home."

Kaidan didn't pull away from my grip, but stared at me for a long moment. His dark hazel eyes studied me as if searching for the truth of my words. I knew that he wanted to believe me—wanted to think that I'd come back from that mission, but the struggle was still raging in his mind, and probably in his heart as well.

I squared up to him and shifted my hands to his shoulders. "Shepard…" He began to protest weakly, but I silenced him with my lips on his. Soft at first, then more demanding, more passionate. I wanted him not just to believe me, but to believe _in_ me like he had when I was his commander and he was my lieutenant. I pulled him in close and pressed my body against his, urging him on, waking up those quiescent hormones. My fingers fumbled at the waistband of his trousers, slipped inside to grab and stroke and arouse.

Kaidan groaned, but he was beyond protesting. His own hands cleared a space on the desk and then lifted me onto it. He spread my legs to stand between them and put a rough, strong hand under the black fabric of my shirt, working up to feel the hardened nub of my nipple.

We kissed again, like a wave crashing on a cliff, unstoppable and powerful. His lips tore at mine and his hands grew even more frantic, reaching for my pants, pulling them off, shoving the underwear aside to stroke my soaked sex.

I freed his arousal from his pants and guided him to the correct position. Kaidan looked deep into my eyes and thrust, without asking permission, without any gentleness or tenderness or regret. I dug my nails into his scalp and raised my hips to take in all of him. I could feel his anger and hurt over my absence in every deep thrust, and it felt better than anything I'd ever known. It was primal and urgent and _right_.

The only sound in the room was my panting and his occasional muted grunting. I wrapped my legs around his waist, the pressure building within me.

"_Harder,"_ I commanded with a harsh whisper in his ear. Kaiden obeyed. He held my hips firmly against the edge of the desk and pounded me with thrusts that seemed to shake the whole Citadel. I came on the third one, and he on the fourth, after which he stopped and breathed deeply and steadily into the sweaty hair at the nape of my neck—just filling me, emptying into me, shivering next to me.

We stayed like that for a moment—much too short of a moment—and then Kaiden pulled out and tucked himself back into his trousers. He stood back but didn't meet my gaze while I skimmed into my black fatigues pants and straightened my top. When I was done I reached for his hand, but he drew back.

"I'm sorry Shepard…I don't know what this is…"

"It's just me Kaidan." I said. I couldn't keep the vehemence out of my voice. After all that, he was still unsure? He was _sorry_? "It's me and you and sex. It's nothing that hasn't happened before."

He still avoided my eyes. He was backing towards the door. Retreating.

"Don't you dare leave. I'm not done talking to you Alenko!" I said in my most intimidating commander's voice.

"I see now what your idea of talking is. It was a dirty trick tracking me down here just for…your sick pleasure. I don't want to be with you like that Shepard. It's not right."

"You could have said that before you started fucking me." But I knew it was lost.

"I'm sorry, Shepard. No amount of sex can make up for those lost years." Kaidan's hand was on the control panel.

And he was gone. Just like that, again. Gone.

#

His next letter was another apology. I only read a few lines, and then I deleted it. What did I need some messed up biotic who said he didn't want to be with me immediately after having sex in a desk in a C-sec office?

My mood was foul for days and I took it out on everyone else. Jack told me to fuck off (and not in her friendly way), Samara locked me out of the starboard observation deck, and even cool-tempered Garrus told me to piss off after I rudely criticized his work in the Battery. It wasn't until Mordin offered me a hormone-replacement treatment and I made Yoeman Chalmers cry that I realized what a bitch I was being.

Dr. Chakwas called me to the med bay and I went. I felt sort of deflated after all that anger. Empty.

She studied me with her calm, serious eyes. "Commander, are you feeling alright?"

I sat beside her at the desk. Part of me wanted to tell her to fuck off and mind her own business. But another part of me wanted her advice. She had known Kaidan back on the Normandy SR-1. She was older and wiser than me, and I knew that she could hold her tongue.

"I got dumped, Doctor," I said finally.

The Doctor looked around, confused. "Ehm…Excuse me Shepard, I wasn't aware that you were in a relationship."

"Kaidan and I started sleeping together back on the SR-1. I thought we would just pick up where we left off but…" I opened my hand palm up and then let it fall like the pieces of my broken romance.

Dr. Chakwas was silent, studying me, probably riffling through her memories of me and Kaidan, remembering everything I had said about him, and him about me. Her brows lifted as if in sudden understanding.

"Didn't you see Commander Alenko on Horizon too?"

"We kissed on Horizon and it was just like old times…but then he rushed off and wrote me a message apologizing for it. Then I tracked him down last time we were on the Citadel. We talked, we fucked, and then he apologized and said that there was no way it could work out between us."

Dr. Chakwas put her hand on her chin. "I can see how that would be upsetting to you. When a man does one thing and then says another it can be very frustrating."

"You worked with Kaidan Doctor, do you think he's serious about not being with me?"

"From what I remember, Kaidan was always a rather serious young man. I treated him for his migraines on several occasions, and battle wounds besides. He wasn't one to complain, but he did seem rather indecisive at times. Maybe he's sending you mixed signals because he truly doesn't know what he wants."

"How can I make him understand?"

Dr. Chakwas leaned back in her seat and took a deep breath. "You're not going to like hearing this, Commander, but you can't _make_ anyone do anything when it comes to romance. There's no magic combination of buttons you can push to make Kaidan fall in love with you."

"I'm not stupid Doctor, I know that." I could feel my defensiveness rising. Dr. Chakwas was lucky I didn't have my assault rifle with me. No. I needed to stay calm. She wasn't trying to rile me. She was giving me her heartfelt advice. She knew me and she knew Kaidan. I had opened myself up to her.

"All I'm saying is that you have to give it time. Kaidan is going to do what he's going to do. Focus on yourself and your missions. Take some R&R when you have a chance."

"I don't have time for R&R." I said shortly. I crossed my arms over my chest and brooded.

"If we have time to go on all of these side-missions to gather your team and earn their respect, then ought to have time to make sure our Commander is in her right state of mind. Besides, I thought that were all just killing time until we could get the IFF functional and installed anyway."

I jutted my jaw disagreeably, but I knew that the Doctor was right. I wasn't being fair to the crew when all I was doing was blowing around the ship like a solar storm, shorting out everything in my path.

"We'll see." I said. I stood up and headed for the door. "Thanks for the talk Doctor." But even after the talk, I only felt marginally better.

#

Time. Time was my enemy and my friend. I had lost time while I slept dead and dreamless on a Cerberus operating table, and now I had to kill some time while EDI and the techs got the IFF installed. Timing, in a gunfight, can be measured in milliseconds. When it was on your side and that shot landed at just the right moment when your target was reloading or taking aim it was glorious—and when it was against you and the bomb blew just as you were about to cross the bridge it was a nightmare.

But as the Doctor predicted, time eased my anger and resentment. I did a heist with Kasumi, I helped Liara defeat the former Shadow Broker, and then I went to visit the crash site of the Normandy SR-1.

"Commander, it appears that there's already a shuttle at our preferred landing zone. It's Alliance."

"Find another landing zone and give me the coordinates. Anderson must have put someone else on the job too."

"Right away Commander."

I kept my voice steady, but my heart was thumping loud and hot in my ears. The only other person I could imagine Anderson sending to the Normandy crash site was…

Kaidan. I knew it was him before I stepped off of the Kodiak. He stood in his armor under the falling snow, his head turned to look up at the twisted wreckage.

His hand went to his gun, but he must have known I was coming or his orbiting ship would have shot me out of the sky on my way in. His hand dropped to his side. His face would have been hard to read beneath the face plate if I didn't know him so well. As it was, he was contemplative. Not angry, but not happy either.

"Shepard. How…have you been?"

"I'm standing in the wreckage of crash that killed me, with the man I loved who rejected me. I've had better days Alenko." My voice was honest, lacking the poison and vehemence of our last meeting.

"Hackett sent me to gather the dogtags of the fallen. We know basically who all died, but it's still a gesture of assurance to have the physical evidence. He said something about a monument too."

"Of course. I've got the monument in the shuttle. Help me drag it out to the clearing and I'll help you search for the tags. Two sets of eyes are better than one. Unless you're a Batarian, that is."

He smiled at my joke and then followed me to the storage compartment to lug the monument out. His biotic field did the majority of the work, and soon the weatherproof, ultra-durable monument was situated. It would last for centuries, a marker for the graves of those who had fallen in Alliance service, at the hands of the Collectors. Technically that included me.

Kaidan and I stood in silence for a moment contemplating and remembering. Joker just had to try to save the Normandy one more time. I just had to go back for Joker. The last explosion just had to be seconds before I could get into the escape pod. Time again, that time it had been my enemy, and it had cost me two years of my life.

"Do you know what I did when Joker told me that you didn't make it?" Kaidan asked, breaking the silence.

I didn't answer. I didn't really want to know.

"I punched him. I wanted to break both his legs and then throttle him with my biotics, but the bastard felt so bad about it himself that he would have enjoyed the punishment too much. As it was I broke his jaw. It was wired shut for a month."

"Yeah, poor Joker. Poor you." I scoffed. I didn't mean to belittle his pain—well, yes, I did. I wanted him to be over it already. I wanted him to realize that he needn't have felt so bad. I wanted him to see me as I was now and accept that I was back, and take advantage of this rare opportunity to have the person you loved _not_ actually be dead after all.

But he continued as if I hadn't interrupted him with a bitchy comment. "I took on some pretty rough missions in that year after. I thought if you were dead, then anyone could die. And I didn't mind that it might be me next. The crew scattered, I got promoted for one of those damn risky missions, and I started to move on. I stuck to what I knew—the Alliance, biotics, special ops—and the more I acted like myself, the more I started to feel like myself."

"I see you went back to talking way too much." I said. Still he ignored me.

"My friends even convinced me to go on a date. There was this doctor on the citadel…"

I snapped my head around, jealousy blossoming in my gut. "Who?"

"It didn't work out, don't worry Shepard. She wasn't…she wasn't you."

"If she wasn't me, and I'm not me, then what the fuck are you looking for Kaidan?" I said, exasperated.

He turned to me and took my hands. I was expecting another apology, more stalling, another long rambling speech about how the passage of time can do strange things to a person's heart.

"You are you, I see that now. I know that I said that sex couldn't make up for those lost years and I stand by that, but maybe we can just get over those years instead of trying to make up for them."

His hands were heavy in mine, even through the thick armored gloves we both wore. He had said it, almost word for word what I wanted to hear. And yet…standing here in the wreckage of the SR-1 made Kaidan seem so small and the crash seem so big. I had pushed it to the back of my mind, skipped over the unpleasant reality that I should be dead. My dogtags should be hidden somewhere in the snow here. My name should be plastered on some tablet commemorating the fallen. Yet here I was.

"Let's get looking," I said. I didn't know what to say, and fortunately Kaidan didn't press me. We started a slow circuit of the crash site, stopping every now and then to gather a bit of glinting metal confirming a death, or to stare in awe at the huge hunks of metal which were once part of the most advanced military vessel in the galaxy.

Finally we finished the circuit. "How many IDs do we have?"

"I think they're all accounted for. Thanks for your help Shepard."

"These people…they all lost their lives fighting the Collectors. More will fall after them, no doubt. I've even gave up my life in the line of duty. The only thing I've held onto, the only thing that I've wanted more than defeating the Collectors…" I looked into Kaidan's eyes, intense under heavy brows, "Is you Kaidan."

I turned away and lifted my eyes to the swirling colors of the planet's aurora above us. "I guess I have to let go of that too. I have to give my whole self to the mission. I can't keep any piece in reserve for love."

"Shepard...don't talk like that."

"Come up to my cabin on the Normandy. Be with me tonight like we were on our first night."

There was silence behind me, then a hand on my waist, heavy and armored to keep out the cold and the lack of atmo. But I could feel it, and it gave me hope.

"If I spend the night with you, I won't want to ever leave," Kaidan said. I could hear the heartbreak in his voice.

"What's wrong with that?"

"I'm Alliance, Shepard. I have duties and responsibilities. I can't abandon them any more than you can abandon your mission against the Collectors."

I knew he was right, and I also knew that if he was the kind of man to abandon his post I wouldn't love him like I do. But it hurt just the same, right or wrong.

"I should go." I said, shrugging his hand off of my waist.

"So this is goodbye then?" Kaidan asked.

"Looks like." I tried to keep my voice nonchalant, but Kaidan knew me too well. He probably saw the agony in my eyes even through the orange tint of my helmet's visor.

"When you come back from the Omega 4 relay…" Kaidan began.

"I'll find you Kaidan. I promise."

"And I'll wait for you Shepard, I promise."

* * *

_Epilogue_

_A few weeks before the beginning of ME3 (Slight Spoilers for beginning of ME3)_

Blowing up an entire Batarian System, good reason or no, had a lot of political consequences. I lay on my bed, fully dressed, frowning at the ceiling of what was essentially a cell. Grounded. Shipless. Crewless. Rankless. Back from the dead and yet still in purgatory, figuratively speaking. I tried to imagine it as a nice relaxing break from shooting people and blowing shit up, but I couldn't, not when I knew that the Reapers could descend upon us at any moment. Imminent danger, and yet here I was with my thumbs up my ass because of damned _politics_. At least I had a nice view from my window. After years of ship duty it was nice to wake up to Earth's clear blue skies.

The door to my chamber whooshed open and I glanced over, expecting some young star-struck guard to escort me to the next hearing about my court-martial. I nearly jumped when I saw that it was Kaidan.

He looked good, hardly worse for wear in the almost year since we had talked at the Normandy SR-1 crash site. Still tall, dark, handsome, and broody. I sat up and smiled, elbows resting on my knees.

"Commander Shepard," he said. "May I come in?"

I motioned to the only chair in the room. He sat stiffly, as if visiting me was an uncomfortable duty that he couldn't worm his way out of.

"You found me," I said with a smile, alluding to our conversation in the Amanda system. "Did you get my comm message?" I wasn't willing to just let him forget that little promise we exchanged and then broken. After returning from the Omega relay, I hadn't called him up and taken the Normandy off to be with him. I had done my duty—the one that he had accused me of shirking—and reported back to the Systems Alliance headquarters on Earth to pay for the consequences of my escapades. And he…well it was obvious that he hadn't waited for me.

"I did. I wasn't able to get back here any sooner though, and I'm sorry. How…how are you?"

I stretched my arms over my head and let my gaze wander to the window. "Better than the last time we talked. I'd ask you how you are, but I hear congratulations are in order. Spectre Major Alenko,"

He smiled and shook his head. "You paved the way for that Shepard. You were the first human Spectre, and you're the one who taught me what it means to command. I do owe you."

"You don't owe me a damn thing Kaidan. The galaxy needs you. I long since let go of any chance of us being together. Some things just aren't meant to be." My voice was cold, calculating, distant. I'd had hours of solitude to think over what I was going to say in this moment. But Kaidan's shocked expression sent me reeling, dropped my heart down into the pit of my gut, and threatened a lump very like a sob in the back of my throat.

"Shepard…" He seemed at a loss for words. I stood up and went to the window, leaned on the frame, looked out over the tops of the buildings that made up the Alliance Headquarters.

"Why did you come here Kaidan? You could have just sent a message."

He was quiet for a moment. I didn't look back at him. I didn't want to see him hurt, and I knew that I had hurt him. I had meant to.

"I came here to see you. I thought…" he stood up and turned towards the door. "I thought maybe you still had feelings for me."

"Feelings?" I turned to him, anger finally boiling up around my sunken heart, down in my gut, flaring into flames. "Kaidan, I loved you. I threw myself at you. You had a chance and you blew it. So don't act like some victim here."

"I'm not, Shepard. I know I screwed up. I should have…damn, but I was such an ass about you being with Cerberus. If it weren't for Cerberus you wouldn't even be here—and look what you've done. I doubted you, and I'm sorry."

The lump in my throat finally rose up and hacked its way out. The anger boiled up and turned to tears, which I tore from my face. I advanced on Kaidan until his back was against the door, my face only inches from his. I knew I must have looked like a madwoman—eyes red and crazed, voice cracking with emotion, my new haircut mussed all to hell.

"That's all I wanted to hear all along. And now it's too late."

I smashed my palm against the control panel. The door opened behind him and I shoved, hard, with both hands on his chest, forcing him backwards out the door. He stumbled back a few steps before catching himself. The door closed before he could say another word. That was it. We were done.


End file.
